Phantom Mysteries
by mystery writer5775
Summary: Bones calls the two best paranormal experts in on a case, but what happens when the clues start to lead them to the missing Danny Fenton and Danny Phantom...
1. the smoking skeleton

**this is a special story i did because apperantly there are no Bones DP cross over fics. i dont own DP or Bones**

_**Line break**_

Bones walked onto the newest crime scene with Booth at her side.

They quickly stepped over the rope to see what had happened "what's the damage" Booth asked.

A cop came up and walked by them "don't know, some one just called about hearing screams, we pulled up and found this" he said as he motioned to the scene in front of them.

They stopped dead.

There was a crater in the ground and in the middle was a skeleton that was still smoking.

It also had some glowing green goop on it and around it "what do you think of this" the cop asked.

Bones shook her head in confusion "I'm not sure" she said.

She slowly got down and collected some samples of the goop and bones "this is stranger than I've seen, even more so than that glowing skeleton" she said.

Booth threw up his hands "so when do we call in the paranormal experts" he joked.

Bones looked at the stuff thoughtfully "actually I believe my cousin studies this kind of stuff, she studies the paranormal and as much as I believe other wise, this looks kind of like what she studies" she said thoughtfully.

Then she got up "however she might be hard to get over here" she said.

Booth crossed his arms and he and Bones began walking back to the car "why is that" he asked.

Bones shrugged "her son disappeared a few months ago, she just walked into his room and he was gone, no note or anything, just vanished" she said.

Booth laughed "you can't just vanish, can you?" he asked.

Bones got in the car, Booth quickly followed "that's the thing, he did" she said.

Booth started the car "what's your cousins name" he asked.

Bones looked at him "Fenton, Maddie Fenton, she's a scientist in the paranormal scientists, and she has this ridiculous notion that ghosts exist though clearly it must just be an illusion of the mind do to some fact or another" she said.

Booth quietly drove to the Jeffersonian, deep in thought.


	2. Danny

**i don't own DP or Bones!**

_**line break**_

Back at the lab Bones gathered her team "okay new case, we have a skeleton covered in a glowing green goop, Hodgins you are to find out what that stuff is, Angela you are to find out who this person was, and Zach" she paused.

Booth stepped up "find something to do" he said.

Zach looked around in confusion as Bones and Booth headed into her office.

One hour later all three of them came into Bones' office with notes.

Angela stepped up first "this doesn't make sense, I've crossed referenced the bones and came up with some psychiatrist named Penelope Spectra who has been dead for seven years, Zach on the other hand found something else" she said.

Zach stepped up and put some X-rays up "this person was just killed yesterday in a flash fire, like literally maybe five seconds of flame at most, another strange thing though is that these burn marks are way different than I have seen yet, they aren't from a normal fire" he said.

Finally Hodgins walked up with a folder that held some graphs "and from what I can find this substance that was on the bones is purely ecto plasm, although I did find minute traces of human blood to a teenager named Daniel Fenton" he said.

Bones quickly grabbed the charts to see "are you sure they belong to Daniel Fenton" she asked.

Booth looked up at Bones in surprise "didn't you say your cousins last name is Fenton" he asked.

Bones nodded and took out a picture of a raven haired teen "Danny Fenton is her son" she said.

_**Line break**_

Bones paced in her apartment on the phone.

After three rings someone picked up.

Booth walked up since it was on speaker "_you've reached Fenton Works, Sam Manson speaking_" someone said.

Booth cleared his throat "well Samantha is this the Fenton residence" he asked.

They heard a low growl "_first off it's Sam, call me Samantha again and I will hunt you down, and yes this is the Fenton residence, may I ask who's calling_" she asked.

Bones laughed slightly "my name is Temprance Brennan, please excuse my partner Booth, I'm a cousin of Maddie Fenton and have some information regarding her son" she said.

There was a crash and some yelling on the other line.

Suddenly an older woman's voice came on "Temprance? How are you, is what Sam said true?" she asked.

Bones sighed "hey Maddie, we recently got a crime scene that is in your field and your sons blood was identified at the scene" she said.

They heard another crash "is he…dead" Maddie said fearfully.

Bones sighed "no, the bones we found were from a Penelope Spectra, she was also covered in a glowing goop one of my team identified as ecto plasm, but since your sons blood was found I have two offers, one is to come down here and help me solve the case, the second is to come down here to help tell us all you can about your son" she said.

There was a pause "we'll come, but I am bringing my husband, daughter, and my sons two friends" she said.

Booth snorted "why? They would just be a hindrance to the case" he said.

Bones glared at him "ignore him, but honestly why?" she asked.

They heard a sigh "my husband studies ghosts as well and Jazz won't rest until Danny is found and his two friends Sam and Tucker have ran away until Danny is found" she said in a tired voice.

Bones sighed "okay, so call me when your flight comes in and me and Booth will pick you up" she said.

Maddie giggled "oh so your still working with Booth are you, is that the guy who was talking earlier, you ought to take the advice I told you three months ago" she said.

To Booth's surprise Bones actually blushed a bit "I've got to go, bye" she said before hanging up.


	3. Missing bones

**i don't own DP or Bones!**

_**Line break**_

The next day Bones stood by Booth at the airport waiting for the Fenton's.

suddenly they saw a rugged looking group walking towards them.

In front was a young Gothic girl who was walking angrily as though it was a forced trip "one question, which of you was it that called me Samantha" she asked first thing.

Nervously Booth slightly raised a hand "are you a cop of any kind" she asked.

Booth nodded slowly "FBI" he said.

Sam made the little watching you sign as Maddie came up "please be nice Sam" she begged.

Then she gave Temprance a hug that completely startled her "it's so good to see you again, still studying bones like back when you were little?" she teased.

Bones smiled "actually I'm the head forensics at the Jeffersonian Institute along with my partner Booth who is in the FBI" she said.

Maddie smiled lightly before frowning "did you find anymore information on Danny" she asked quietly.

Bones looked at Booth "perhaps we should go back to the lab" she said.

Maddie nodded sadly "and this time Bones, I'm driving" Booth said.

Maddie looked confused "it's a nickname I've earned, everyone around here calls me that" she said.

Slowly they headed out to the car and drove to the Jeffersonian.

Once there Bones directed them towards her office.

She looked at the family in front of her "Danny's blood was taken from a living person which means he was alive when the blood was taken, however the blood was moved from who knows where, from what I can tell the blood may have been moved from anywhere in the US, however it does show a distinct possibility that Danny is alive" she said.

Tucker looked up "how, all you got was one small blood sample" he asked.

Bones looked at her notes "the way the blood was set up it almost looks as though Danny is the killer or victim of the scene, obviously someone either wants to frame him to get some crazy revenge or make it look like he's dead for their own purposes" she said.

Tucker, Sam, and Jazz exchanged nervous glances "who was the victim" Maddie asked warily.

Bones looked at her notes again "a Penelope Spectra…" she stopped as the three teens snickered in laughter "what" Bones asked.

Sam stepped up "I'm sorry but Penelope Spectra is dead, she was one of the ghosts haunting our town" she said.

Bones looked thoughtful "that would explain how she died twice and was covered in ectoplasm, but I have one question, how could ghosts exist" she asked.

Maddie rubbed her forehead "it's like I said when we were younger, ghosts are a bunch of post human consciousness created after a person dies who still has work to do in the world" she said warily.

Bones shook her head "and like I said, it's impossible, they would have to have some big enough imprint on the planet with their spirits that could rival the face of God" she said.

Maddie rolled her eyes "not true for some ghosts can actually be very weak and even the strongest ghosts have a weakness like Phantom, a ghost who used to terrorize our town, has been captured though who ever captures him are usually forced to free him so he can help save the others we know in one way or another" she said.

Bones held up a hand "okay a few things I noticed, first, _used_ to? You act as though he just stopped protecting the town or something, and second, if he is terrorizing then how come your forced to free him for his help?" she asked.

Maddie stopped "I guess your right about the help, and as for used to, he vanished around the same time as Danny, according to Sam and Tucker who apparently know him, he's trying to find Danny, though I wouldn't even see why he cares" she said.

Booth looked at the nervous kids who twisted in their seats "can I have a quick word with Sam and Tucker" Bones asked.

Maddie nodded and she motioned for the two of them, and Booth, to follow.

They went into a secluded area in the lab. Booth leaned over "now remember Bones, get into it nice and slowly" he whispered.

Bones stepped up "what are you hiding about Danny that you won't tell his parents" she asked.

Booth threw up his arms "so much for being discreet" he muttered.

Sam and Tucker exchanged nervous looks before sighing in defeat "Danny is a unique kid and because of it he has a lot of enemies" Tucker said.

Sam stole a nervous glance at Tucker before nodding.

She pulled out a picture of Danny half way through transformation "Danny Fenton _is _Danny Phantom, he didn't want anyone to know and the only ones who do are standing in this room, and Jazz" Sam explained.

Bones closely studied the picture "how could a person become half ghost, I mean, even if ghosts did exist he must have had a massive shock that affected his DNA' she said. Tucker snorted as Sam's eyes widened "impressive, actually the Fenton's built a portal to the ghost realm and I coaxed Danny to go in after it didn't work, unfortunately he put his hand on the wall and hit the on switch, the portal loaded up and turned on giving him a shock that changed his DNA" she said.

Booth snickered quietly before coughing falsely to cover it up "why didn't he tell his parents" Bones asked.

Tucker looked cross "hello! His parents are ghost hunters! That stupid shock turned him into a half ghost! Not to mention his parents want to rip Danny 'Phantom' apart molecule by molecule!" he said.

Bones nodded in understanding.

Suddenly an alarm went off "not again" Bones said as she ran out of the room.

Booth, Sam, and Tucker followed closely as she ran into the examination room.

The bones were gone.


	4. Wisconson

**don't own DP or Bones**

_**Line break**_

They all gathered around the security cameras watching in wonder as the bones somehow just got up and vanished.

Maddie turned to Bones "still don't believe in ghosts" she teased.

Bones turned and looked at Hodgins "did you find anything new before the bones vanished" she asked.

Hodgins smiled "a few things actually, first there was actually ectoplasm from two different beings, the victim and it looks like some one put the blood of notorious ghost hero Danny Phantom on the bones in the same matter of ways as Danny Fenton's, both clearly trying to make it look like they were dead" he said.

The group exchanged nervous looks "second I found some soil that is only found in one place in the world, Madison, Wisconsin" he said.

Maddie gasped "that's where Vlad lives" she said without thinking.

Booth looked at her carefully "who" he asked.

Jazz stepped forward "Vlad Masters, my parents attended college with him until he contracted ecto acne in an accident, from them he blamed my dad and has a grudge against Danny for some reason" she said.

Jack looked crest fallen "that doesn't sou…" "yes it does" every one else minus Bones and Booth said.

Maddie had a fierce look in her eye "do you have enough for a search warrant" she asked.

Hodgins smiled "more than enough, all we need now is an FBI…" he hinted.

Booth sighed in defeat "so let me guess we have your family, Bones, me, and Danny's little friends" he asked.

_**Line break**_

The next day the seven of them stood quietly in front of the giant mansion with a finger hovering over the door bell.

Booth took a deep breath and rang it.

Instantly it was opened by the confident looking billionaire "FBI, we're here to investigate a murder and kidnapping" Booth said as he showed his badge.

Vlad smiled widely "I'm afraid you need a search warrant to come in" he said slyly.

Booth showed him the warrant.

Angrily Vlad allowed them in "please don't ruin anything" he said as he left a glare towards the three kids.

Jazz smirked and turned to them "if he has Danny I know where Danny would be, he has a hidden basement I accidentally found while staying here that is accessible through his private study" she said.

Booth motioned for her to lead the way.

Se quickly led them to the private study and pulled the golden football.

The fireplace opened up to reveal a dark winding staircase "of course always with the dark and winding" Booth said.

Booth slowly led the way down.

As they neared the bottom they heard some weird sounding gun shots and cries of pain "that sounds like our ecto blasters" Maddie whispered.

Behind them Jazz grabbed something from her purse discreetly.

Booth stopped at the corner and listened for a bit "you have been a pain in the neck for the last time" someone said from around the corner.

There was another blast and cry of pain.

Maddie heavily resisted the urge to run out "now your family is here with the FBI! I gave you a choice but you didn't take it so now your going to experience your destruction" the voice said.

Jazz couldn't take it.

She gripped the device in her hand tightly and jumped out from the stair well "hey cheese head" she called as she pushed the button.

Vlad dropped Danny Phantom to the ground as she was enveloped by the Fenton peeler "stay away from my family" she yelled as she shot at Vlad.

The others ran out from around the corner as 'Plasmious' screamed.

Slowly he faded into Vlad Masters causing the others who didn't know to gasp in shock.

Vlad lay weakly on the ground until Sam sucked him into the thermos.

While they did that Bones ran over to Danny and checked his pulse "who are you" he whispered.

Bones did a quick injury assessment "it's okay Danny, I'm your aunt, your family is hear and we're getting you out" she said.

Slowly she helped Danny 'Phantom' to his feet which resulted in him not even being able to stand properly.

Maddie gasped at the sight of the ghost boy, his out fit had been torn everywhere and there was green blood oozing out of several cuts.

Suddenly Danny looked nervously around and began struggling to get away "I came here for a reason, I'm not leaving yet" he whispered.

Startled Bones let go of him and he stumbled over to a locked room.

He unlatched the many locks and opened the door "Danielle" he whispered.

There in the middle of the floor was a young girl with midnight black hair, a blue sweater, and red shorts and baseball cap.

She weakly turned towards Danny and smiled "are we free yet" she asked.

Warily Danny smiled as he stumbled to her.

He leaned down and gave her a hug "yes" he whispered before, in front of everyone, the two rings split along his waist to reveal the long lost Danny Fenton "DANNY!" Maddie yelled.

Danny turned weakly towards her with a tired smile before blacking out.


	5. Epilogue

**Don't own DP or Bones and warning Bones is slightly OOC in this chapter...**

_**Line break**_

Bones sat down in her office one month later with a letter from Amity Park. Carefully she opened it

**Hi Aunt Temprance (or do you prefer Bones?),**

**I wanted to thank you and agent Booth for freeing me and Danielle, although I did hear a slight rumor you don't believe in ghosts, hope this changed your mind! Anyways, I hope Danielle is doing fine with you, I still am very grateful for your decision to adopt her. Vlad is safely behind bars (in the ghost zone of course) and will not be getting out for the next ten thousand years if I remember right. And for the record, I found where little Ms. Spectra went, apparently she still had some haunting to do around Amity, though it is so easy to keep her in check.**

**Hope your doing well, say hi to Danielle for me!**

**Danny**

**PS. If Booth asks, the flowers were your idea…**

Bones smiled and handed the letter to the youth sitting across from her, Danielle had been helping her with many cases and seemed to have a knack for picking stuff up.

Then Bones smiled as Booth walked into the office looking flustered "did you send me flowers by any chance" he asked.

Bones rolled her eyes "yes I figured they would be a great way to show how I feel about you" she said, thinking along the lines of Daisies or something.

To her surprise Booth blushed "Danny did it, didn't he" he asked.

Bones raised an eyebrow "how did you…" "because I got red roses, not some friendship or thank you flowers" he said.

Bones blushed and shot a look at Danielle who vanished "well maybe one person can see we were meant for each other and should try a date" Booth suddenly said slyly.

Bones smiled "pick me up here tonight at eight" she said.


End file.
